malariagen_data.af1.Af1.plot_pairwise_average_fst

Af1.plot_pairwise_average_fst(fst_df: DataFrame, annotation: Literal['standard error', 'Z score'] | None = None, zmin: int | float | None = 0.0, zmax: int | float | None = None, text_auto: bool | str = '.3f', color_continuous_scale: str | List[str] | None = 'gray_r', width: int | None = None, height: int | None = None, row_height: int = 40, col_width: int = 50, show: bool = True, renderer: str | None = None, **kwargs)

Plot a heatmap of pairwise average Fst values.

Parameters

fst_dfDataFrame

A dataframe of pairwise Fst and standard error values. It has 4 columns: cohort1 and cohort2 are the two cohorts, fst is the value of the Fst between the two cohorts, se is the standard error.

annotation{‘standard error’, ‘Z score’} or None, optional

How to annotate the upper-right corner of the plot. Default behaviour (None) is using Fst, other options are using the standard error (if annotation is ‘standard error’) or the Z score of the two cohorts being the same (if annotation is ‘Z score’).

zminint or float or None, optional, default: 0.0

The lower end of the range of values that the colormap covers.

zmaxint or float or None, optional

The upper end of the range of values that the colormap covers.

text_autobool or str, optional, default: ‘.3f’

If True or a string, single-channel img values will be displayed as text. A string like ‘.2f’ will be interpreted as a texttemplate numeric formatting directive.

color_continuous_scalestr or list of str or None, optional, default: ‘gray_r’

Colormap used to map scalar data to colors (for a 2D image). This parameter is not used for RGB or RGBA images. If a string is provided, it should be the name of a known color scale, and if a list is provided, it should be a list of CSS-compatible colors.

widthint or None, optional

Figure width in pixels (px).

heightint or None, optional

Figure height in pixels (px).

row_heightint, optional, default: 40

Height in pixels (px).

col_widthint, optional, default: 50

Width in pixels (px).

showbool, optional, default: True

If true, show the plot. If False, do not show the plot, but return the figure.

rendererstr or None, optional

The name of the renderer to use.

**kwargs

Passed through to px.imshow().